At present when the human genome is disclosed, a pharmaceutical application utilizing the human genome attracts attention. For drug development based upon the genomic information, it is essential to ascertain an interaction between protein (gene) and a compound; however, massive labor is required to experimentally ascertain these interactions. As a prior art for estimating the interaction between protein and a compound, in general, an estimation system using a conformational model is known (Non-patent Literatures 1 to 4). This system is a method to estimate a stable complex structure with ligand and its strength of binding, and it is referred to as a docking study.
In Published Japanese translation of PCT International Publication for Patent Application 2002-530727 (Patent Literature 1), it is described to specify a high activity region in chemical space and to structure a library. However, this method is merely a definition of the chemical space using only chemical information (such as structure activity correlation information or pharmacophore information).
Further, with a conventional method (Non-Patent Literature 5) by the inventor himself, after a compound group and a protein group are statistically processed separately, such as cluster analysis, compound processed data and protein processed data are integrated and they are displayed on a two-dimensional map, and an interaction pair of protein and the compound is presumed.
NIH of the US has started a chemical genomic project as a national project in 2004. Since then, the application of the genomic information to a chemical field has been focused upon over the world but mainly in the US and Europe. Therefore, at least in the developed countries, such as the US, an efficient estimation method is in demand.
[Patent Literature 1] Published Japanese translation of PCT International Publication for Patent Application 2002-530727
[Non-patent Literature 1] Yoshifumi Fukunishi, Yoshiaki Mikami, and Haruki Nakamura. “The filling potential method: A method for estimating the free energy surface for protein-ligand docking” J. Phys. Chem. B. (2003) 107, 13201-13210.
[Non-patent Literature 2] Shoichet B K, D L Bodian, and I D Kuntz. “Molecular docking using shape descriptors.” J. Comp. Chem., 1992. 13(3), 380-397.
[Non-patent Literature 3] Jones G, Willett P, Glen R C, Leach A R, and Taylor R. “Development and validation of a genetic algorithm for flexible docking.” J. Mol. Biol. 1997. 267(3):727-748.
[Non-patent Literature 4] Rarey M, Kramer B, and Lengauer T. “Time-efficient docking of flexible ligands into active sites of proteins.” Proc. Int. Conf. Intell Syst. Mol. Biol. 1995; 3:300-308.
[Non-patent Literature 5] Okuno Y, Yang J, Taneishi K, Yabuuchi H, and Tsujimoto G. “GLIDA:GPCR-Ligand database for Chemical Genomic Drug Discovery” Nucleic Acids Research, 34, D673-677, 2006.